[Bioperl-l] Remote Blast and Report

Ocar Campos ocarnorsk138 at gmail.com
Wed Feb 25 19:03:53 EST 2009


   I'm working in a script to remote blast a file with some sequences, I
already got the part of sending the query to blast, but I do not get the
idea of how retrieve a txt report, I mean, like the one you get by running a
blast via web and you can read in a plane text editor.

This is what I've done so far:

use Bio::Tools::Run::RemoteBlast;
use Bio::SearchIO;

$prog = "tblastx";
$db = "nr";
$e_val = "1e-10";
$remoteBlast = Bio::Tools::Run::RemoteBlast->new(-prog => $prog,
                         -data => $db,
                         -expect => $e_val
                         -readmethod => 'Blast');

#I select the file to make que query and do the blast.
$infile = 'file.input.fasta';
$r = $remoteBlast->submit_blast($infile);

#this should be the report i get.
$outfile = 'got.output';

further than this I've tried some things but none of them work, anybody who
could give an idea of how retrieving the plane text reports please?



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